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TTHHSSEEEn vue de l'obtention du

DDOOCCTTOORRAATTDDEELLUUNNIIVVEERRSSIITTDDEETTOOUULLOOUUSSEE

Dlivr parUniversit Toulouse III (UT3 Paul Sabatier)Discipline ou spcialit :Anthropologie gntique

JURYLARROUY Georges, Professeur mriteHERNANDEZ Miguel, Directeur de RechercheFRANCALACCI Paolo, Directeur de RechercheGARCIA MORO Clara, Directeur de Recherche

GIBERT Morgane, Charg de RecherchePEREIRA SANTOS Cristina, Charg de Recherche

CALO Carla Directeur de Recherche

Ecole doctorale :Biologie Sant BiotechnologieUnit de recherche :Anthropologie Molculaire et Imagerie de Synthse, UMR 5288

Directeur(s) de Thse :DUGOUJON Jean-Michel, MORAL Pedro

Rapporteurs :VARESI Laurent, CALO Carla

Prsente et soutenue par GAY-VIDAL Maria MagdalenaLe 26 Septembre 2011

Titre :Genetic characteristics of the two main Native groups in Bolivia: Aymaras andQuechuas.


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Als meus pares,

na Rosa i en Raimon


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Homo sum; humani nil a me alienum puto:

Sc un home i res del que s hum ms ali

Terenci

"Une chose surtout donne de l'attrait la pense des hommes : cest l'inquitude."

Sobretot una cosa fa suggestiu el pensament hum: la inquietud

Anatole France

No es faria ja cap altre descobriment si ens conformssim amb el que ja sabem.

Lucio Anneo Sneca


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Acknowledgements

Barcelona, 11 June, 2011

After all these years, I have had the opportunity to work in different laboratories,

get to know new people, some of them are true friends. I appreciate all the support of

those that have always been encouraging me.

First of all, I want to thank my supervisors, Dr. Pedro Moral and Dr. Jean-

Michel Dugoujon. I am very grateful to Dr. Dugoujon for offering me the opportunity to

work with an Aymara population for my Erasmus project several years ago, giving me

such an amazing project and keeping me in contact with the lab of Toulouse. When I

first arrived in Toulouse it was impossible for me to think that after all these years Iwould be so attached to this subject that has fascinated me and to the ville rose that

has given me a lot and where I have lived unforgettable moments.Merci beaucoup pour

mavoir dirig la thse avec comprhension et patience.

I want to express a special acknowledge to Pedro with whom I have worked

most of the time and who has always been available whenever I needed help. Thank you

for always encouraging me, even in the most difficult moments. Me has enseado

mucho tanto en el aspecto humano como profesional, muchas gracias.

I would also like to thank all the people of both labs, at Morals lab: Esther,

Marc, Emili, Robert, Ares, Josep and Magda R, thanks for all your advice, help,

exchange of ideas, jokes, conversations, coffee breaks, and everything that makes the

work fun, you are the best company I could ever had. I want to especially thank PhD

Athanasiadis (bazinga!) that has helped me a lot during all these years, always with a

smile. No encuentro ni una sola palabra para expresar mi agradecimiento, gracias

por tu amistad. I want also thank the master students, Albert and Irene, and the visitors

from other countries who have helped to break the routine of the lab, Wifak, Laura P,

Daniela. Also, many thanks to the Moral people I met throughout these years: Toni,

Neus V, Natalia, Meri. Thanks to rest of the people from the Unitat dAntropologia,

Mireia, Neus M and Marta, the Lourdes group (Brbara, Araceli, Mar, Slvia, Marina,

Ximena, etc.), the people from the other coin of the lab, Jordi, Bea, Ferrn, Laura,

Mohammed, Andrs, and, of course, I want to thank all the bosses, Lourdes, Clara,

Miquel, Alejandro, Daniel, and Txomin. Moltes grcies tamb al Dr. Pons pel seu bon


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humor.All of you are the main reason that I have really enjoyed to work in our lab all

these years.

Although I have been more time in Barcelona than in Toulouse, I know that I

have good friends there. At the lab of Toulouse, I would like to thank the PhD students I

met when I arrived as an Erasmus student, Stphane (I remember him encouraging me

when I was trying my pulse not to trembling too much when charging a gel) and

Clotilde for her patience and good explanations. The following years I met Harilanto,

Nicolas, Nancy, Laure, Beatriz (another visitor, la otra espaolita); in addition to their

good company in and outside the lab, they have always helped me a lot to solve the

distance issue. Its a pleasure to know that I have such good colleagues and friends

over there. I want to thank also Mr. Larrouy, Denise L, Line H, Andr S, Morgane G,

Eveline G, Cathie T, and especially to Mr. Crubzy who accepted me for doing my

Erasmus stage at the lab. Merci beaucoup tous pour me permettre partager une

partie de ma thse avec vous dans un laboratoire o je me suis sentie comme chez mois,

pour votre convivialit, et bien sr, pour tous les apros.

I can not forget the three-moth stay in London. I am very grateful to Dr. Andrs

Ruiz-Linares from the UCL for accepting me at his lab and making me feel like home.

There, I meet Barbara, Tbita, Karla, Andrs, Desmond, Mari-Wyn, many thanks for

sharing all those moments with me, without you that stay would have not been the

same.

From outside the labs I have received a lot of support throughout these years

from all my friends. In Barcelona, thanks to Clara, Maite, Marta, Ana, Diana, Laura G,

Sergi, Laura S, Slvia, for listening to me, and being comprehensive when I am stressed

(only good friends can do that!). From Mallorca, I want to thank Marga S, Marga G and

Vicky for their true friendship. Also I want to thank my class mates from the

Bioinformatics master, for their help and support during these last months, Yorgos of

course, Jos Luis, Pascal, David, etc.

Finally, and the most important of all, I want to thank my family, my parents

(Rosa and Raimon), and my sister Mia for all their support and courage they have given

to me.Moltes grcies a tots tres per sempre animar-me i estar al meu costat donant-me

tant damor, fent que tot aquest cam fos ms fcil ; and special thanks to Jose, for his

help and lots of patience. Grcies per compartir amb mi els moments ms difcils, per

tamb els ms felios, com aquest.


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TABLE OF CONTENTS

FOREWORD...................................................................................................... 5

KEYWORDS...................................................................................................... 6

INTRODUCTION................................................................................................ 7

I.1. The place...............................................................................................................................................7I.1.1 The Americas .................................................................... .............................................................. 7I.1.2 The central Andes ............................................................. .............................................................. 8I.1.3 Bolivia.............................................................................................................................................9

I.2. Brief history of Native Americans: archaeological and historical records. ..................................10I.2.1 The first Americans.......................................................................................................................10I.2.2 The central Andean region ........................................................... .................................................11I.2.3 Bolivia...........................................................................................................................................19I.2.4 Demographical Data......................................................................................................................20

I.3 Linguistic data.....................................................................................................................................21I.3.1 The Americas .................................................................... ............................................................ 21I.3.2 South America...............................................................................................................................23I.3.3 The central Andes ............................................................. ............................................................23

I.3.3.1 Quechua.................................................................................................................................25I.3.3.2 Aymara ........................................................... ................................................................... ....26I.3.3.3 Other minor languages .................................................................... ......................................29

I.4 Other cultural and environmental aspects of the Andean populations..........................................31 I.4.1 Altitude environment ......................................................... ...........................................................31I.4.2 Economical organization...............................................................................................................32I.4.3 Social organization........................................................................................................................33

I.5 Human genetic variation....................................................................................................................34I.5.1 Human population genetics...........................................................................................................35

I.5.1.1 Evolutionary processes..........................................................................................................36I.5.2 Genetic markers ................................................................ ............................................................ 38

I.5.2.1 Brief description of the principal markers.......................................................... ...................38 I.5.2.2 Markers used in this work .............................................................. .......................................40

I.6 The peopling of the Americas from a multidisciplinary approach.................................................51I.6.1 Brief revision of the principal models...........................................................................................51

I.6.2 The most recent hypothesis .......................................................... .................................................52I.6.3 The peopling of South America ............................................................. .......................................54

I.7 Populations studied.............................................................................................................................57I.7.1 The Aymara sample .......................................................... ............................................................ 58I.7.2 The Quechua sample .................................................................... .................................................59

II. OBJECTIVES .............................................................................................. 60

III. RESULTS ................................................................................................... 62


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III.1 Supervisors report on the quality of the published articles........................................................62

III.2 Results I: Gay-Vidal et al., 2010.......................................................... .........................................63

Autosomal and X Chromosome Alu Insertions in Bolivian Aymaras and Quechuas: Two

Languages and One Genetic Pool ................................................................. ..........................................63

III.3 Results II: Gay-Vidal et al., 2011..................................................................................................73

mtDNA and Y-Chromosome Diversity in Aymaras and Quechuas From Bolivia: Different Storiesand Special Genetic Traits of the Andean Altiplano Populations........................................................73

III.4 Results III: Gay-Vidal et al., (manuscript 3)...............................................................................89

APOE/C1/C4/C2 Gene Cluster Diversity in Native Bolivian samples: Aymaras and Quechuas ......89

IV. DISCUSSION ........................................................................................... 109

IV.1 Genetic characterization of the two Bolivian samples ................................................................ 109IV.1.1 Data provided for the first time in Native Americans .............................................................. 109IV.1.2 Within-population genetic variation.........................................................................................110IV.1.3 Admixture of Native Bolivian populations ................................................................. .............112 IV.1.4 Particular genetic features of the current Bolivian populations................................................113

IV.2 Genetic relationships between the two Bolivian samples............................................................116IV.2.1 Linguistics vs.genetics in current Bolivian Andean populations.............................................116 IV.2.2 Introduction of Quechua into Bolivia.......................................................................................117IV.2.3 Sex-specific population histories..............................................................................................118IV.2.4 Concordance between different markers ................................................................ ..................118

IV.3 Genetic relationships among South Americans...........................................................................119IV.3.1 Genetic relationships between the two Bolivian samples and other Native Americans ...........119 IV.3.1 Genetic relationships among Andean populations ................................................................. ..119

IV.3.1.1 Genetic relationships among Central Andean populations...............................................120IV.3.2 Genetics vs.linguistics ............................................................. ................................................122IV.3.3 Geography vs. genetics.............................................................................................................123

V. CONCLUSIONS ........................................................................................ 125

VI. REFERENCES ......................................................................................... 126

VII. APPENDIX .............................................................................................. 145

VII.1. Supplementary material of Gay-Vidal et al., 2011 ................................................................. 145

RSUM........................................................................................................ 151

ABSTRACT ................................................................................................... 152


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Foreword

The Andean highlands have been the cradle of complex societies and several

amazing civilizations that still fascinate us. A legacy of that are two of the most spoken

Native American languages (Aymara and Quechua). Another particularity of this

region, as impressive as its population history, is an environment of altitude with hard

living conditions, to which highlanders are biologically adapted.

In the past decades, as genetic studies emerged, a new world of possibilities

appeared. Since then, a lot of studies have tried to elucidate the questions about human

populations from a genetic point of view, complementing other more traditional

approaches as archaeology, history, and linguistics. Several genetic studies on Andean

highlanders have been focused on providing a better knowledge of the genetic basis of

adaptation to altitude. However, other aspects of these populations, like their genetic

relationships, are also interesting.

In this context, the present work is a genetic study of two populations of the two

major Native linguistic groups (Aymaras and Quechuas) from the Bolivian Altiplano.

The first section of this work, the Introduction, situates the present work into a general

context. The introduction has seven parts: the first part is just an introduction to the

Americas, the central Andes and Bolivia; the second part is a historical section, giving a

brief revision to the history of the Americas based on archaeological and historical

records; a third part treats the linguistics. These sections will introduce a general

knowledge to the Americas, although focusing on South America and the Andean

region in particular. The fourth part deals with cultural and environment aspects of

Andean populations. The fifth part is dedicated to the human genetic variation,

including a description of the most important concepts in human population genetics

and the contribution of genetics to the history of the America, in particular South

America and the Andean region. In the sixth section the models about the peopling of

the Americas are revised, and the final part gives a detailed description of the two

populations studied here.


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The Introduction is followed by the goals of this work, in the Objetives section.

The Results section contains four parts. The first one is the report of the supervisors

about the quality of the published papers, and three remaining sections, each one

corresponding to an article accompanied by a brief summary in Catalan. The first article

is about Alu insertions in the two Bolivian samples, the second article, contains the

results obtained for uniparental markers, for both the mtDNA and the Y-chromosome,

and the last one consists of an article about the genetic variation on the

APOE/C1/C4/C2gene cluster region. Finally, there is the Discussion section and the

Conclusions. A summary in Catalan and French is also added.

KeywordsAymaras

Quechuas

Native American

Andean populations

Bolivia

Mitochondrial DNA

Y-chromosome

Alu insertions

APOE/APOC1/APOC4/APOC2


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INTRODUCTION

I.1. The place

I.1.1 The Americas

The Americas, also known as the New World, have always awakened a special

interest in different disciplines, probably due to the fact that they were the last continent

to be populated. However, this fact has not implied that unravelling the mysteries of the

peopling of the Americas is easy. Far from that, controversy still exists in all fields that

have tried to answer the questions related to this topic (archaeology, linguistics,

morphological and genetic anthropology).

South America on its own bears

such a high complexity at different

levels, that a lot of studies in different

fields have focused only on it. South

America could be divided into several

cultural geographical regions: Andes,

Llanos, Amazonia, Chaco, Pampa, and

Patagonia (Figure 1). The Andean

region, presenting one of the most

fascinating and incredible histories, as

well as a particular environment of

altitude requiring biological

adaptations, is particularly interesting.

Culturally, the Andes can be divided

into three areas, North (Ecuador,

Colombia, and Venezuela), Central

(Peru, Bolivia and North Chile) and

South (Chile and Argentina) (Figure 1).

Figure 1. South America cultural areas (Stanish, 2001).


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I.1.2 The central Andes

The central Andean region is geographically divisible into three areas: 1) the

lowland area to the east of the Andes, heavily foliaged and connected to thewesternmost part of the Amazonian jungle, 2) a dry, arid coastal plain crossed by

several rivers flowing from east (Andes) to west (Pacific), and 3) the sierra or

highlands, the rugged mountains of the Andean chain. It was in the last two areas where

the first complex societies appeared and where the major civilizations of South America

flourished (Stanish, 2001).

The Altiplano, a plateau enclosed between the

two Andean chains, at an average altitude of ~3658

meters above sea level (m.a.s.l.), (3000-4500

m.a.s.l.), is where the Andes reach their maximum

width. The most part is located in Bolivia, but also

it occupies part of southern Peru and areas of

North Chile (Figure 2). In the border between Peru

and Bolivia, we find the Lake Titicaca at 3811

m.a.s.l., the larger lake in South America.

The idea that the central Andean region presents a cultural homogeny is generally

assumed, probably due to the fact that when the Europeans arrived, the Inca Empire

covered this region entirely, promoting the cultural unity of the Empire, and the

Quechua language was present in most areas (imposed by the Incas). Nevertheless,

before the Inca Empire, distinct cultural, linguistic, and political areas characterized this

region.

Figure 2. The Andean Altiplano.


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I.1.3 Bolivia

Bolivia is a country located in central South America bordered by Peru, Chile,

Argentina, Paraguay and Brazil that has an area of 1,098,580 Km

2

. Its landscape can bedivided into three topographical and ecological parts, the Altiplano, the Yungas, and the

Lowlands (Figure 3).

The Lowlands (Oriente) cover two-thirds of the country in the eastern (Chaco

plains) and northern part of Bolivia.

The Yungas is a humid, rainy and warm area between the highlands and the

lowlands in the eastern slope of the Cordillera Real of southern Peru and Bolivia. The

valleys, mountains, and streams contribute to the presence of very diverse forests,

becoming a rich environment.

The Andean Altiplano is located in the western part of the country. Almost half of

the population lives on the plateau that contains the capital La Paz (3630 m.a.s.l.), as

well as two other big cities, Oruro and Potos (4090 m.a.s.l.). Distinct dry and rainy

seasons give birth to the Puna grassland, the ecosystem found in the Altiplano as well as

in the central Andean highlands. The Puna is found above the tree line at ~3500 m of

altitude and below the snow line at 4500-5000 m.a.s.l., resulting into a cold region with

low oxygen diffusion. It is drier than the pramo of the northern Andes. Native

mammals of the Puna are alpacas, llamas, vicuas, and guanacos.

Fi ure 3. Bolivian landsca e.


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I.2. Brief history of Native Americans: archaeological and

historical records.

The history of the population of the Americas can be split into two main periods:the Pre-Columbian period, extended from the first settlements of the Americas to the

arrival of Columbus in 1492, and the historical period that can be divided into three

stages: the conquest, the colonial and the post-colonial times.

I.2.1 The first Americans

In 1590, Friar Jos de Acosta already argued that Native inhabitants of the

Americas must come from Asian populations (Acosta, 2002). Although nowadays it is

widely accepted that Native Americans came from East Asia through the Bering Strait

at some point during the last glacial maximum (LGM) when the sea level was much

lower and Asia and America were connected, the time, routes, and the number of waves

that entered the New World still remains uncertain (see the I.6 section).

The time of the entrance of the first humans in the Americas has been under

discussion among archaeologists for decades. Until recently, it was thought that the first

migrants entered the New World ~11,500 BP according to the Clovis-first-model. This

model, based on the Clovis arrow points (stone tools that have been found in most

archaeological sites in North America), proposed that hunter-gatherers colonized the

continent leaving behind traces that have permitted to date their passage to Mexico,

Peru, Chile until the Southernmost part of Argentina, the Patagonia, where remains

were found dated back to 11,000 BP (Salzano and Callegary-Jacques, 1988) and that

leaded to the extinction of the mammalian mega-fauna. These data indicated that the

first settlers of the Americas colonized the whole continent from current Alaska to

Tierra del Fuego in some thousand years.

However, new archaeological sites and revision of previous ones have proved a

pre-Clovis settlement, opposing to the Clovis-first theory. One of the most important

sites is Monte Verde in Chile dated to 14,700 BP (Dillehay, 1997). Other important pre-

Clovis sites (Meadowcroft, Page-Ladson, and Paisley Cave) in North America also

indicate a presence of humans in the Americas from ~15.2 to 14.1 ka. Although less

certain, it is important to mention possible sites dating earlier than 15 ka (Cactus Hill)

or even older, between 19 to 22 ka, (La Sena, Lovewell) (Goebel, Waters, and


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ORourke, 2008). Finally, a recently discovered site in Texas dated back to 15.5 ka

(Pringle, 2011).

Archaeological data have proved that the eastern part of Siberia was populated

around 32 ka, indicating that modern humans had learnt how to subsist in this extreme

environment. In the eastern part of Beringia, some remains have been proposed to have

about 28 ka old, according to some archaeological sites. However, the earliest reliable

remains date back to 14 ka in current Alaska. The coastal corridor seems to have

deglaciated and permitted human habitation by 15 ka, and the interior corridor until 14

to 13.5 ka (Goebel et al., 2008).

After the discovery of the Monte Verde site, the fact that, before 15.7 ka, the ice

covered completely Alaska and Canada and therefore there was a margin of only ~1000

years for the journey from Asia to Chile on foot, the Pacific-coast theory appeared.

Fladmark (1979) proposed that crossing the two continents (12,000-mile trip) in only

1000 years could be possible travelling along the Pacific coast by boats. However, this

theory is difficult to prove since sea level has risen, inundating the coastline. Another

proposed model has been the Atlantic coast route, as the highest concentration of Clovis

artefacts is found in the eastern part of North America, indicating a higher population

density in the East than in the interior of the continent as expected according to the

traditional model.

I.2.2 The central Andean region

According to archaeological records, the human settlement of the central

Andean region could be traced back to around 10,000 BP and has continued until

present.

Pre-historic times can be divided into several periods (Stanish, 2001): A pre-Ceramic and an Initial period followed by three Horizons -Early, Middle, and Late-

which are characterized by pan-Andean cultures (Chavn, Tiwanaku-Wari, Inca).

Between the Horizons, two intermediate periods (Early, Late) took place with

flourishing regional cultures.

ThePre-Ceramic period (10,000-2000 BC) is characterized by the movement

of hunter-gatherers as evidenced by archaeological remains in Peru around 8000 BC. In

the late pre-ceramic period, several cultural sites with important monuments (pyramids,


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walled plazas, etc) have been found indicating the first sedentary people and the

development of the first complex societies according to ranked societies reported in the

Pacific coast of Peru (Guayaquil, Peru, 5000 BP; Caral, Peru, 4600 BP, etc). In the

highlands, a ritual tradition, known as Kotosh Religious Tradition, was developed

(Kotosh, La Galgada, Peru 2300 BC). The architecture of the coast and the highlands

was different; however, exchange networks existed between the coast, the highlands

and the eastern slopes.

The Initial period (1800 BC- 900 BC) is characterized by the development of

new technologies (ceramic, metallurgic, agriculture and farming) as well as social

institutions. The social complexity grew up to reach the formation of hierarchic

societies. During this period, regional cultures (e.g. Kotosh, 2300-1200 BC; Cerro

Sechin, 1000 BC; Paracas, 800 BC) took place. In the highlands, the important

civilization of Chavn started in Chavn de Huantar in central highland Peru around 900

BC, becoming a centre of elite pottery, textile and stone art. It is important to mention

the first construction in the south central highlands, the Chiripa site located in the south

of the Titicaca basin (1300 BC).

The Early Horizon(900 BC- AD 200) corresponds to the first pan-Andean art

style known as Chavn in the highlands and the coast, representing the first well-

documented culture. A general collapse of polities occurred in the coast, while the

cultures of the highlands in the north central Andes prospered and the site of Chavn

increased in size and power. It has been suggested that by that time the population was

2000-3000 people, making Chavn an important political centre. Its influence reached

the region of the current city of Ayacucho, Peru (Sondereguer and Punta, 1999). Other

highland sites also grew in size and complexity; in the south central highlands the

Pucara site dominated the northern Titicaca basin from 400 BC to AD 200. Pucara artshows links to the contemporary coastal Paracas (800-100 BC) in the Ica region, and

Early Tiwanaku, with antecedents in Chavn. There is controversy about whether

Chavn and Pucara should be considered states or not. Many agree that these sites were

just ceremonial centres, while others consider them as complex chiefdoms or regional

political spheres. In the southern Titicaca basin, Tiwanaku was occupied at this time,

but its size and complexity is unknown.


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The Early Intermediate (AD 200-600) is characterized by more regional

cultures. In the north coast, the Moche culture appeared (AD 400). Moche site was

unequivocally a true city, dominated by two main pyramids, Huaca del SolandHuaca

de la Luna. It may be the first Andean city and the first time there is evidence of royal

tombs in the Andes. In the south coast the Nazca culture appeared (AD 100-800),

whereas in the south central highlands, the Pucaraended as a political centre around

AD 400. Finally, in the Titicaca basin of the Altiplano, the Tiwanaku site grew in

importance and power, becoming a state.

The Middle Horizon(AD 600-1000) is characterized by the coexistence of the

two first states. As shown in Figure 4, the Tiwanakucivilization (100 BC-AD 1000)

extended from Lake Titicaca to the south central Andes, while Wari (AD 700-1000)

extended from Ayacucho in south central Peru to the northern highlands (Blom et al.,

1998; Sondereguer and Punta, 1999).

In the south central highlands, around AD 600, Tiwanaku started an expansion

process in the western part of Bolivia, Southern Peru, North Chile and North-Western

Argentina. The site of Tiwanaku is a vast planned urban capital. In AD 800-900

Tiwanaku presented an impressive architectural core (pyramids, streets, temples, state

buildings) surrounded by adobe houses of artisans, labourers, and farmers. It has been

estimated that it covered an area of 4-6 km2, with a population in the Tiwanaku valley

ranging from 30,000 to 60,000 (Stanish, 2001). Areas of intensive agricultural

production have been detected. Also, Tiwanaku colonies have been found in Moquegua,

Cochabamba, Larecaja, and Arequipa. The Tiwanaku state seems to have controlled

politically and militarily-strategic areas such as roads, rich agricultural areas and

regions with high resources, indispensable to maintain such a population.

In the north central highlands, the Wari culture originated in Huanta (Ayacuchoregion) and expanded until reaching the Cuzco area in the South and Cajamarca in the

North. The Wari urban complex has been calculated to cover an area up to 15 Km2, the

core site presenting a similar size than the contemporary Tiwanaku.

As a conclusion, around AD 500 the first states with a road network, warrior

elite, and capitals, existed in the Andes. Around AD 1000, Tiwanaku and Wari had

large populations, planned urban capitals, socioeconomic classes, expansionist policies,

economical specialization, and colonial sites. The relationships between these two


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contemporaneous (coexisting around 500 years) and neighbour civilizations, whether

they were in conflict, competition or just complementary are in great part hypothetical

and controversial (Owen, 1994; Sondereguer and Punta, 1999; Isbell et al., 2008).

The high degree of complexity and the population density reached in the central

Andean region was possible thanks to the Vertical Archipelago Model (Murra, 1972).

This model explains how different environment regions (the coast, the highlands, and

the yungas) provide abundant and varied resources.

Figure 4. A) Extension of Wari and Tiwanaku civilizations (taken from Wikipedia-based on Heggarty,

(2008)). B) Detail of the Tiwanaku influence area (Kolata, 1993).

The Late Intermediate orlate regional developmentperiod (AD 1000-1476).

At the end of Wari and Tiwanaku states, a period of regional cultures re-emerged

(Chanca, Cajamarca, Chincha, Chim, local states in the Altiplano, etc) (Figure 5A).

The end of Tiwanaku, between AD 1000 and 1100, was due to the agricultural collapse

because of a dramatic decrease in precipitations and the beginning of a drought period.

The cities around the Titicaca Lake disappeared for nearly 400 years and human

populations dispersed in smaller groups, starting a period of political instability. The


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twelve Aymara kingdoms or seorosidentified (Bouysse-Cassagne, 1986) established

in a deep politic-economic-territorial reorganization are shown in Figure 5B. Two of

these kingdoms (Qolla, Lupaqa) seem to have been organized almost at the state level

with colonies in the coast and yungas. When the Incas irrupted by the mid fifteenth

century, these two groups were in a battle for the political supremacy of the Lake

District. Thus, if the Incas had not invaded these territories, probably a new Tiwanaku-

style empire would have started (Kolata, 1993).

Figure 5. A) Map of the regional cultures of the late regional development period (image taken

from Wikipedia). B) The location of the Aymara polities (image taken from Graffam, 1992).

The Late Horizon period (AD 1476-1535) corresponds to the Inca Empire

(1438-1532AD), also known as Tawatinsuyu. A prevalent theory says that the Inca

civilization derives from a family group probably from the Titicaca region that moved

northwards to the Cuzco city in the 12th

century (Markham, 1871). From Cuzco, the

Inca Empire, in contrast to Tiwanaku, expanded its power towards the North and South

with calculated military violence and coercive techniques such as language imposition


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(Quechua) and community displacements (mitma system). These strategies inevitably

awakened the hostility against the Inca Empire. At the arrival of the Europeans, the Inca

territory expanded from the South of current Colombia in the North to Chile in the

South (Figure 6A). This vast territory, the Tahuantin-suyu, was divided into four

provinces or suyus: Chinchasuyu, Antisuyu, Contisuyu, and Collasuyu (Figure 6B).

Figure 6. A) The Inca expansion. B) The four quarters of the Inca empire (taken from

Wikipedia, based on: A: Rowe, 1963, and B: Kolata, 1993).

The Inca Empire was characterized by the construction of a complex road

system that communicated the whole empire. Their architecture is also impressive; theconstructions were built using stones sculpted that fit together exactly. The site of

Machu Picchu is the most famous Inca construction.

The Incas carried out the mitma system (mitmaq meaning outsider or

newcomer), deliberate resettlements of people, sometimes even entire villages, for

different purposes (colonize new territories, work). They also used the mita system

(mitameaning turn or season), a mandatory public service to carry out the projects

of the government such as building the extensive road network, construction of


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Emperor and noble houses, monuments, bridges, temples, working in mines and fields.

Also military service was required some days out of a year.

The social organization was highly hierarchic. At the highest level of the social

pyramid was the Emperor, the son of the sun, with an absolute power and supposed to

have a divine origin. The nobility occupied the highest administrative, military, and

religious functions. The local chiefs could continue to be the authority if they were

faithful to the sovereign. The labourers at the bottom of the pyramid included the

farmers in general as well as the mitimaes.

The Conquest and Colonial period

In 1531, the Spaniard Francisco Pizarro arrived in Peru and in 1532 entered

Cajamarca and captured the Inca Emperor Atahualpa. In a few years (1531-1536), the

Spaniards succeeded in conquering the Inca Empire. The fact that in many regions the

Europeans were seen as liberators from the Incas has been suggested as a reason for this

rapid disintegration of the Inca Empire. With the arrival of the Spaniards, a lot of

villages were funded (Chuquisaca, nowadays Sucre, La Paz, etc) including the capital,

Lima.

In 1542, the Viceroyalty of Peru was created, including most Spanish-ruled

South America (Figure 7A). Laws that protected the autochthons were created, although

never applied. In 1568, several decades after the invasion, the true colonial period

started with the arrival of Jesuits and of Viceroy Francisco de Toledo (Murra, 1984). In

1717, the Viceroyalty of New Granada was created, in 1742, the Viceroyalty of the

Capitaneria general de Chile, and in 1776, the Viceroyalty of Rio de la Plata. The

region of current Bolivia, known as Upper Peru, became part of the Viceroyalty of Rio

de la Plata (Figure 7B).During the colonial period, a big effort was made to convert the natives to

Christianity; even native languages (Quechua, Guarani) were used, contributing to the

expansion of these tongues and providing them with writing systems. Natives served as

labour-force under the mitasystem taken from the Incas in mining industry or haciendas

owned by Spanish colonials. In 1545, Potos, a mining town, was founded and in few

years became the largest city in the New World with a population estimated of 120,000

people, with constantly arriving people under the mita system from the entire Andes


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(Cruz, 2006). From there, large amounts of silver were extracted from Cerro Rico, near

Potos, becoming an important revenue for the Spanish Empire.

In the end of the 18th

century and beginning of the 19th

,important revolts took

place against the Spanish authorities in all the colonial territory.

Figure 7. A) Viceroyalty of Peru and itsAudiencias. B) Viceroyalties in 1800.

The Republic Period

In the beginning of the 19th

century, the independence from Spain was declared

and after a long period of wars, the independence was established and several republic

states were created (Paraguay, 1811; Uruguay, 1815). The insurrectionary army led by

Simn Bolvar won the Independence of Nueva Granada (current Venezuela and

Colombia), Ecuador and Bolivia (named in honour for Simn Bolvar) by 1825, and

Jos de San Martn that of Argentina (1816), Chile (1818) and Peru (1821).


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I.2.3 Bolivia

In Bolivia, the decades after the independence were characterized by political

instability, where revolutions alternated with military dictatorships. Moreover, Boliviahad to face several conflicts with frontier countries (Chile, Paraguay, and Brazil) that

led to the loss of half of its territory after one century of independence. In particular, the

Pacific war (1879-1883) between Chile and Peru and Bolivia was especially cruel with

Andean people as it took place in their territory. In this war, Bolivia lost the province of

Atacama and their access to the sea. In the beginning of the twentieth century, Bolivia

lost the Acre region against Brazil and ceded part of the Chaco region to Paraguay in

the Chaco war (1933-1935).

In the mid-20th

century democracy was established and the government carried

out important programs promoting rural education and agrarian reforms. However,

migration from the countryside to urban centres has been constant, depopulating the

rural area. Currently, 67% of total population (10.1 million people) lives in urban

centres. Additionally, as the highlands experienced an excess of population, highlanders

started to migrate to the lowlands (Mojos plains in Beni department, Bolivia).

At present, Bolivians are mainly of a native origin (~55%), 30% being Quechua

and 25% Aymara speakers, both groups located in the Andean region of the country.

Other native groups are the Guaranis, Mojeos, Chimanes, etc, living in the lowlands.

Around ~30% of Bolivians are mestizo (mixed Native and European ancestry) and

around 15% from European ancestry (Sanchez-Albornoz, 1974; www.cia.gov on 5

May, 2011).

In recent years, movements have risen claiming the recognition of Native rights

throughout the Americas and especially South America. A particular case is Bolivia,

where in 2005 Evo Morales was the first indigenous descendant (from Aymara origin)

elected president of the country.


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I.2.4 Demographical Data

There is great disagreement on the size of the Native population of South

America when Europeans arrived; the proposed population sizes range from 4.5 to 49million. An approximation proposed in Crawford, (1998) is shown in Table 1.

Table 1. Population of the Americas at the arrival of the Europeans.

North America 2 million

Central America 25 million

Caribbean 7 million

South America 10 million

Total 44 million

At the arrival of the Europeans in South America, the high population density of

the Pacific coastline and the mountains contrasted with other less populated areas

(Snchez-Albornoz, 1974). Considering the estimates proposed by Salzano, (1968) of

about ~10 million South Americans, the inhabitants of the Inca Empire have been

calculated to be about 3.5 million with the highest density in South America (10 people

per square mile) (Crawford, 1998).After the contact with Europeans, a dramatical depopulation took place due to

war, epidemics caused by European diseases to which the Natives had no resistance,

hard conditions by forced labour, etc. The depopulation ratios presented high variation

depending on the region. Some groups became extinct while others could eventually

recover.

The population of Native Americans decreased from over 44 million to 2 or 3

million in less than 100 years. This drastic reduction of the Native American gene pool

from 1/3 to 1/25 of their previous sizes implied a great loss of genetic variation, that is,

a genetic bottleneck. Therefore, the current Native populations, descendants of the

survivors, may present different frequency distribution of some genetic traits

(Crawford, 1998).


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I.3 Linguistic data

As peoples migrate, separate, and isolate, their genetic patrimony diverges, but

also their culture, including the language. From the study of the relationships amonglanguages, the relationships of the peoples who spoke them can be inferred. Linguists

have tried to classify world languages into families based on comparative linguistics.

The field that studies the genealogical relationships between languages and family

languages is the genetic linguistics. The linguist Johanna Nichols proposed that at least

20,000 years, possibly even 30,000 years would have been necessary to produce the

large amount of diversity of languages among Native Americans. Although at present

most linguists are pessimistic about the use of their data to reconstruct ancient

population histories beyond about ~8 ka (Goebel et al., 2008), some works

complementing linguistics and archaeology seem to be useful to reconstruct

approximate time-scales and the geography of language expansion in the last thousands

of years (Heggarty, 2007, 2008).

I.3.1 The Americas

One of the most controversial areas of genetic linguistics is the classification of

Native American languages. Greenberg suggested three families, Eskimo-Aleut, Na-

Dene and Amerind families (Figure 8). The Eskimo-Aleut would belong to the large,

more ancient Eurasiatic family, together with the Indo-European, Uralic, Altaic,

Korean-Japanese-Ainu, and Chukchi-Kamchatkan families. The Na-Dene family, first

identified by Sapir in 1915, is a family included into a larger one called Dene-

Caucasian, including also Basque, Caucasian, Burushaski, Sino Tibetan, and Yeniseian.

The Amerind family groups together the Centre, South, and part of North American

languages. This family includes eleven branches: Almosan-Keresiouan, Penutian,

Hokan, and Central Amerind in North America, and Chibchan-Paezan, Andean, Macro-

Tucanoan, Equatorial, Macro-Carib, Macro-Panoan, and Macro-Ge, most of them

restricted to South America (Ruhlen, 1994).


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Figure 8. Distribution of the linguistic families in the Americas proposed by Greenberg et al.,

1986 (image from Ruhlen, 1994).

Linguists have criticized this grouping into only three families. Most

controversies are in the classification of the language families of South America.

Campbell believes that this macrogrouping is unjustified, indicating that South America

probably exhibits more genetic and typological diversity than North America and

Mesoamerica put together. We will mention the three main classifications proposed by

Greenberg (1987), Loukotka (1968), and Campbell (1997).


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I.3.2 South America

Greenberg (1987) grouped all South American languages into one stock

(Amerind) including four clusters (Chibchan-Paezan, Andean, Equatorial-Tucanoan,and Ge-Pano-Carib). His classification has mostly been used by human biologists to

hypothesize about the peopling of America. Contrarily, Loukotka (1968) proposed 117

independent families grouped into three categories (Andean, Tropical Forest, and Paleo-

American). Since he did not specify their relationships, it seems more a geographic or

an anthropological clustering rather than a linguistic one (Adelaar and Muysken, 2004).

On the other hand, Campbell (1997) proposed a conservative classification lacking an

internal structure because, as most linguists, he thinks that the data and methods used by

Loukotka and Greenberg are insufficient to establish these relationships.

However, the position of the Andean family in the Greebergs classification is

not clear since in his first classification (Greenberg, 1959), the South American

languages were divided into three groups: Ge-Pano-Carib, Andean-Equatorian, and

Chibchan-Paezan, the Andean and the Equatorian subfamilies grouped together because

Andean languages showed a small distance with Arawak, suggesting the tropical forest

as the cradle of the Andean family; and more recently, the Andean family has been

grouped with the Chibchan-Paezan family resulting in the following three groups:

Andean-Chibchan-Paezan, Equatorian-Tucanoan, Ge-Pano-Carib (Greenberg and

Ruhlen, 2007).

I.3.3 The central Andes

The Andean family includes two of the most spoken Native American language

families, Quechua and Aymara. Quechua is the most widely spoken language family in

the Americas, with more than 10 million speakers in Ecuador, Peru, southern Bolivia,

northern Chile, and Colombia; and Aymara has almost 2.5 million speakers, mainly in

Bolivia, but also in parts of Peru and Chile (Lewis, 2009). Moreover, in the south

central Andean highlands, other languages were widely spoken (Uru-Chipaya, Pukina)

and nowadays are endangered or extinct. Linguists have proposed different theories for

explaining their origin, antiquity, and relationships (see Browman, 1994; Itier, 2002;

Goulder, 2003; Adelaar & Muysken, 2004; Heggarty, 2007, 2008).


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Figure 9. NeighborNet Showing semantic

lexical divergence of Aymara and

Quechua (Heggarty, 2008)

The relationship between Aymara and

Quechua is still on debate. Some studies

supported that the two languages were

genetically related by an ancient proto-

Quechumaran (Orr & Longacre, 1968), or that

the two groups could be included into a family

named Quechumaran (Mason, 1963). More

recent linguistic reports suggested that they are

separated enough to be considered separate

families and if once there was a proto-

Quechumara ancestor, it would be to an

extremely ancient period that linguists can only

speculate (Heggarty, 2008). Figure 9 shows the

level of diversity within and between the two

linguistic groups.

In any case, it is unquestionable that there has been a strong contact between

Aymara and Quechua due to long periods of mutual influence from the beginning,

resulting in high similarities (Heggarty, 2008).

Although the expansions of Quechua and Aymara have been attributed to the

Inca period (Late Horizon) and Tiwanaku (Middle Horizon) respectively, there is strong

consensus among Andean linguists that the ancestor language of the two families

started diverging long before the Late Horizon and probably before the Middle Horizon

too, maybe even by a millennium or so. Moreover, Quechua did not appear in Cuzco or

Aymara in the Altiplano; rather, proto-Aymara and proto-Quechua languages would

have originated in Central Peru (Heggarty, 2008).


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I.3.3.1 Quechua

Although traditionally one talks about Quechua language and its dialects,

Quechua is a linguistic family of unintelligible languages (Itier, 2002; Heggarty, 2007).The Quechua family is divided into two groups of languages (Figure 10): Quechua I (or

Central Quechua) in central Peru and Quechua II (or Peripheral Quechua) including: i)

II-A, in northern mountains of Peru, ii) II-B, in Ecuador (Kichwa), north Peru and

Colombia, and iii) II-C, in South Peru, Bolivia and Argentina (Torero, 1983).

Figure 10. Distribution of Quechua dialects (from Wikipedia, based on Heggarty, 2007)

Quechua, always linked to the Incas, did not appear in Cuzco, and its expansion

is very much older than the Inca period (Itier, 2002). In fact, it is likely that about a

millennium before the Incas, Quechua had had a more ancient pan-Andean distribution.

Heggarty (2007) proposes that Quechua would have arrived in Ecuador some centuries

before the Incas as lingua franca for trade purposes, and the Ecuadorian populations

having an origin language would have adopted Quechua.

The most probable geographical origin of Quechua seems to be Central Peru that

corresponds to present Central Quechua. Finding a more precise location is difficult.

Torero proposed the central coast, in the area of formation of proto-Chavn cultures,

Cerrn-Palomino proposed a further inland location, even the early pre-ceramic site of

Caral (3000-1600 BC) for a pre-proto-Quechua. According to Heggarty (2007), data on


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the degree of diversity per unit area points out to a region in the highlands near Lima, in

the Yauyos province were the first language split it is supposed to occur.

The degree of divergence of Quechua family is comparable to that of Romance

languages, therefore, a similar time-frame has been proposed. That is, the Early Horizon

(900 BC-AD 200) that would coincide with the Chavn culture in the highlands and

coast of north-central Peru, where a proto-Quechua form would have acted as lingua

franca spreading to North and South occupying the distribution that nowadays presents

Central Quechua and would have been an ancestor of the Quechua I spoken in Peru

(Kolata, 1993; Goulder, 2002). However, possible dating could go back up to two

millennia BP or even more (Heggarty, 2007). From there, Quechua spread to the North

reaching Ecuador and to the South (Heggarty, 2008).

In the 15th

century, the Incas adopted Quechua as the language of their empire

probably since it already was a vehicular language; a language of communication

between regions, also a language of privilege, and it was probably their second or

perhaps their third language. In fact, some authors propose a regional form of Aymara

as the language of the Inca nobility, and at an earlier stage Pukina (Heggarty, 2007).

In any case, the Incas spread the Quechua II-C dialect imposing it as the official

language of the empire. Subsequently, during the Colonial period, the Spaniards

continued to use it as lingua franca(it was spoken in the mines, on haciendas, and in

commerce), thus, Quechua II-C expanded to the South, in Peru and Bolivia, where is

currently spoken (Itier, 2002).

Despite nowadays Quechua is an official language, together with Spanish in

Ecuador, and also with Aymara in Peru and Bolivia, it is relegated to a second place.

I.3.3.2 Aymara

Aymara is composed of two branches: a) Central Aymara or Tupino, spoken in

central Peru, in the semi-desert mountains of Lima department, in the province of

Yauyos, where there are two clusters of isolated villages that speaks Jaqaru and Kawki.

Central Aymara is spoken by no more than a thousand people and are in process of

extinction. Some authors consider them separate languages and others close dialects; b)


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Southern Aymara or Collavino, spoken in the Altiplano with three dialects, Huancan,

Tiwanaku, and Oruro (Cerrn-Palomino, 2000; Heggarty, 2008).

Nowadays, Aymara is spoken by ~1.6 million of Bolivian-speakers, 500,000

Peruvians and 30,000 speakers in Chile, although before the spreading of the Quechua

language, the Aymara distribution covered a wider extension than today as it is shown

in Figure 11 (Tschopik, 1963; Itier, 2002).

Figure 11. Distribution of Aymara and Uru-chipaya (Adelaar and Muysken, 2004).

The fact that the currently Aymara-speaking area closely overlaps with the

influence area of Tiwanaku made some authors assume that Aymara was the language

of Tiwanaku, and therefore the time-frame of the Aymara expansion would be the Early

Intermediate and Middle Horizon, and the Aymara homeland, the Tiwanaku itself (Bird

et al., 1984). However, the low diversity within Aymara in the Altiplano is inconsistent

with an expansion as early as Middle Horizon and thus, with a Tiwanaku homeland. In

this way, Central Aymara shows a higher within diversity per unit of area than Southern

Aymara, indicating that the Central Aymara region is probably closer to the original

Aymara homeland. There is agreement among important Andean linguists that Aymara

did not originate in the Altiplano, but in the central-south coast of Peru. Torero (2002)


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proposed the southern coast (the area of Paracas culture). Moreover, the main Aymara

expansion was likely not to be carried out by the Tiwanaku Empire. Both Torero (2002)

and Cerrn-Palomino (2000) associate the other Middle Horizon civilization, Wari,

with Aymara rather than with Southern Quechua.

According to Heggarty (2008), as the diversity analysis between the two

Aymara branches is similar to that found in the Quechua family, the time-frame for the

Aymara divergence would be similar to that of Quechua; that is, a span of more than

one millennium, but probably less than three.

Torero (2002) associates the first Aymara stages with Paracas and Nazca. A first

expansion towards the high sierras would have occurred around the fourth or fifth

centuries due to the cultural influence exercised over the sierra, the Nazcaisation of

the Ayacucho region that would have taken the language of the Nazcas because of its

prestige.

In the sixth century, around Ayacucho, the Wari state extended to the south of

the Cuzco area, and to the North towards the north-central highlands, and influenced the

coast. The second and main wave of Aymara expansion, between 500/600 and 1000

AD, would have been carried out by the Wari expansion, promoting Aymara as state

language. Aymara would be present throughout the central-south Andean mountains.

Quechua remained in all the northern area. To the South there was a greater expansion

of Uruquilla and Pukina according to Torero (Itier, 2002).

Then, which was the language of the Tiwanaku people? Kolata (1993) proposed

a multilinguistic scenario in which, at the time of Tiwanaku, three languages were

spoken in the area (Uru-Chipaya, Pukina, and proto-Aymara), the herders would be the

Aymara-speakers but without indicating whether the proto-Aymara or Pukina was the

original language of Tiwanaku. A multilingual scenario with several languages has alsobeen proposed, each one restricted to an area of the society (Quechua: administration,

Aymara: trade, Pukina: religion, and Uru: landless and lower classes) (see Browman,

1994). Other authors support that the people of Tiwanaku more probably spoke Pukina.

According to Torero, Uruquilla was the first language of the Tiwanaku people.

Although Aymara was not the language of Tiwanaku, during the late Tiwanaku period

(contemporary with the Wari), Aymara was already being spoken in these areas because

of the relationships between the two empires. Maybe Tiwanaku acquired Aymara in the


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process of development of the state and finally, the Wari empire contributed to the

Aymara spread (Itier, 2002).

In the Altiplano, the Aymara would have spread relatively late, during the Late

Intermediate from the southernmost Peru, where, by the end of Middle Horizon, there

would be a strong Aymara presence due to the Wari expansion. Although a specific

motor for an expansion at that time (Later Intermediate) is unclear (Heggarty, 2008),

some authors have speculated about it. Cerron-Palomino (2002) suggested the

expansion of the group of Aymaraes in the upper basin of the River Pachachaca

(Aprimac) displaced by Southern Quechua speakers. Torero (2002) also proposed

stages and regions through which Aymara reached the Altiplano.

In any case, Aymara extended at the expense of other indigenous languages of

the Altiplano, where two other families (Pukina and Uru-Chipaya) were widespread

enough (Heggarty, 2008).

Although the Incas imposed the Quechua language, after the Spanish conquest

Aymara was still spoken in small regions of southern Peru, a fact that suggests that the

scenario was a continuum between the two present-day branches (Heggarty, 2008).

However, both Incas, and later, Spaniards favoured the Quechua expansion.

I.3.3.3 Other minor languages

In the sixteenth century, the Andean Altiplano housed other linguistic groups

like Uru, Pukina, Chipaya, Urukilla, Changos, and Camanchaca. The relationship

between these languages is still controversial for linguists; whether they are separate

languages or the same language is referred with different names. Uru-Chipaya and

Pukina are grouped in the Arawak linguistic family. Some authors consider that if Uruand Pukina were considered the same linguistic group, they could be relicts of a

previous Pukina civilization (Browman, 1994). According to Torero, the Pukina was

the language of Pukara (city and ceremonial centre to the north of Lake Titicaca) that

was important before the rise of Tiwanaku around 100 AD, and Uruquilla was the first

language of the Tiwanaku people. Other authors propose Pukina as the best candidate to

be the Tiwanaku language (Heggarty, 2008).


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In any case, in the late-prehispanic period, Uru-Chipaya was spoken in the

shores of Lake Titicaca, Lake Poop and along the river Desaguadero, as well as on the

Pacific coast and North Chile. These people fished and foraged and represented about

25% of the Colla region. At present, some one thousand people speak Uru-Chipaya in

the shores of Lake Popo. Until recently, there were also speakers in the Lake Titicaca

but they have shifted to Aymara. Pukina is now an extinct language (Kolata, 1993;

Browman, 1994; Itier, 2002), but during the Spanish colony, documents attest Pukina

speakers in southernmost corner of Peru where some Pukina toponyms are found

(Heggarty, 2008). It is important to note that some Andean languages have disappeared

during the Spanish colony, Pukina in 1780 (another dating is 1910), even in the 20th

century, Mochica in 1940 (Goulder, 2003).

Table 2. Association between languages and cultures (taken from Goulder, 2003).

Hegemony Language/

family

Main

Dissemination

Comment

Chavn-

Pachacamac-

Chincha-

Inca- Spanish

Quechua 500 B.C.- 1940s

A.D. (today)

9 lives! 9 golden periods!

Pukara to 1780 Pukina 600 B.C. -100

A.D. (c.1750)

Seminal to Tiwanaku and War. Also in

Jesuit/Franciscan missions (See Churajon)

Nazca -Wari Aymara 400-900 A.D

(today)

In some ways now stronger than Quechua,

not in numbers, but sense of unity, circuits

of capital etc.

Moche Mochica 0-600 A.D Last speaker 1940s

Tiwanaku Uruquilla 400-600 A.D(today)

Still spoken in Chipaya, Bolivia

Shipibo-Conibo (Pano) N.A. Up and downstream from Pucallpa


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I.4 Other cultural and environmental aspects of the Andeanpopulations

I.4.1 Altitude environment

When talking about the Andean populations, we inevitably think about the

altitude environment. Since the eighteenth century, naturalists and scientists have

described how highlanders were more tolerant and better adapted to the hypoxic

conditions extant above 3000 m than low-altitude natives who tend to suffer the

mountain sickness. The lower rate of oxygen diffusion from air to blood implies several

physiological responses in the following processes (the ventilation within lungs, oxygen

diffusion, oxygen transport, and diffusion from blood to tissues; Beall, 2007).

A lot of studies have described the morphology and physiology of the Andean

Natives. Several traits have been suggested as characteristic of these people, although

not all of them are necessarily adaptive characteristics: enlarged chest, increased lung

capacities, relatively hypoxia-tolerant VO2max, blunted hypoxic ventilatory response,

elevated haematocrit, increased pulmonary diffusion, preferential utilization of

carbohydrates as fuel, etc (Rupert and Hochachka, 2001).

It is important to distinguish the process of acclimatization from genetic

adaptation. Acclimatising to hypoxia consists on some physiological adjustments

involving an increase respiratory rate as well as the heart rate with a faster distribution

of the oxygen. In the long exposure to altitude, the production of red blood cells is

increased, the oxygen affinity of blood is slightly decreased, and the number of

capillaries is increased.

Since this area has been inhabited for more than 10,000 years, and is highly

populated, it is reasonable to think that there has been enough time for natural selection

to act, and thus, consider Andean people to be genetically adapted. Recent studies have

tried to identify specific genes involved in the Altitude adaptation (Stobdan et al., 2008)

and detect natural selection (Beall, 2007).


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I.4.2 Economical organization

The rural Altiplano economy has been based on two important sectors: herding

and agriculture, these two activities showing such an important interdependency that inthe literature the most used term is agropastoral economy. Each community (Ayllu) is

engaged in both pastoral and agricultural activities.

Even though at first glance, the windswept, arid plains of the Altiplano seem to

be an inhospitable place to agriculture, crop agriculture in the lake basin has been

important and highly productive for different kinds of potatoes, native grains like

quinoa and caiwa, and legumes. Since ancient times, terraces were constructed and

sophisticated technologies were developed for intensifying agricultural production.

Highlanders learned how to make the most of the hard climate conditions (the

temperatures drastically vary from warm during the day to freezing at night) for food

preservation. The dehydration (freeze-drying) of staple food, potatoes and other Andean

tubers, permitted a long-term storage, necessary since their production is seasonal.

Pastoral activities predominate above 4000 m with llama and alpaca herding.

This activity has played an important role in the economy of Aymara communities since

ancient times. These native camelids provide not only meat, but also important products

like wool for textiles, skin for leather, dung for fuel and fertilizer and they are also used

for the transportation of their goods (Graffam, 1992).

Additionally, other minor resources have been taken from the lake and rivers

(reeds, fish and fowl) and the dramatic ecological changes in close areas have also

permitted to have access to other products as well as commercial activities like trade

(although nowadays most products are sold, not traded) and wage labour (men have

usually migrated seasonally for wage labour).

In fact, the vertical economic strategy refers to this distribution of activities

depending on the altitude, herding above 4000 m, the potato, other tubers, and quinoa

fields over 3000 m, and the maize, coca, and other warm lands crops in regions bellow

2000 m (Kolata, 1993).


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I.4.3 Social organization

The social organization of Andean people is variable and has been adapted to

special and temporary to political and economical forces. The Altiplano populations areusually grouped in communities, called Ayllus, the basic domestic unit. The Ayllu, an

endogamous, patrilineal, corporate kin group, composed of one or several extended

families (Graffam, 1992). Women tend to marry outside, while the recent married men

stay with their parents until the new couple can be established in their own house.

Traditionally, the new house is located in a territory offered by the father of the groom,

but the increasing alternative economical possibilities have involved a decreasing of this

dependent period until reaching the neolocal residence. Usually, the whole family

collaborates economically. In weddings, baptisms, or other social events, other kin

relationships are established by compadrazo. These compadrazo links can be

horizontal or vertical, and people linked by compadrazocannot get married.


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I.5 Human genetic variation

Human diversity is shaped by demographical and biological factors. Darwin was

the first, together with Wallace, to inquire this variation and to think which process orprocesses could be responsible for it. They proposed the mechanism of natural selection

as the process of evolution. Until the 20th

century, this diversity was defined in

descriptive terms, focusing on visible traits, such as body and face morphology, hair

features and pigmentation (physical anthropology). At the beginning of the 20th

century,

the ABO blood group system was discovered, permitting the definition of the first

genetic polymorphism (Landsteiner, 1901). Subsequently, other blood-group systems

were described and in the middle of the twentieth century, proteins were systematically

studied showing differences among human groups.

These first molecular polymorphisms used in the study of human diversity are

known as classical markers. Classical markers are products of DNA after genetic

expression such as blood groups, enzymes and proteins, the human leukocyte antigen

(HLA) system and immunoglobulin allotypes (Lewontin, 1972). These polymorphisms

were detected by electhrophoretic or immunoprecipitation methods and in the 1960s

and 1970s plenty of data on classical genetic markers were available for different

human groups revealing human diversity (Mourant et al., 1976).

The work of Watson & Crick proposing the double-helix model of

deoxyribonucleic acid (DNA) structure and hereditary mechanism in 1953 represented

the birth of modern molecular biology. This new field of biology has experienced a

flourishing development in the past 60 years strongly influencing many relative fields.

Anthropology is one of the fields most deeply impacted by the theory and method of

molecular biology. Thus, the terms genetic or molecular anthropology are used to

designate the subfield that explores human genetic variation.

In the 1980s, new techniques appeared, like Restriction Fragment Length

Polymorphism (RFLP) analysis and the Polymerase Chain Reaction (PCR). The

detection of variation at a DNA level was available whether or not this variation was

expressed, supposing the beginning of the DNA polymorphisms era. During the late

1980s and 1990s, most studies were focused on mtDNA polymorphisms of the Control

Region, and Short Tandem Repeats (STRs).


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In the early 1990s, the Human Genome Diversity Project (HGDP) was organized

to explore human differences by sampling fragments of the genome from a number of

populations across the globe. At the beginning of the 21stcentury, the Human Genome

Project had as goal the sequencing of the complete human genome that concluded in

2003 (Collins et al., 2003).

The last decade has been characterized by extraordinary technological

developments including automated sequencing techniques, allowing scientists to access

human genetic diversity at an unprecedented rate. The DNA chip technology (also

called DNA microarray technology) allows the analysis up to 2 million mutations in the

genome or survey expression of tens of thousands of genes in one experiment. Finally,

todays third generation sequence techniques will beyond any doubt represent a novel,

very promising step for the determination of human genome diversity.

Homo sapiens is a relatively young species that presents less intraspecific

variation than most of other species that have had more time to accumulate genetic

variation. However, the variation among human groups is significant allowing

interesting studies focused on demographical history reconstruction. The most common

polymorphisms are single nucleotide polymorphisms (SNPs), but also, in recent years, a

large amount of structural variation has been detected.

I.5.1 Human population genetics

Population genetics is a field that focuses in the study of populations, not

individuals. Hence, it is important to establish a definition of population. What is a

population? There are different answers, depending on the context.

In population genetics a population is the ensemble of individuals showing a

reproductively unity. All the inhabitants of a population have the same probability tointerbreed among them and present less probability to breed with neighbour

populations. Geographic and environmental factors imply that the distribution of

individuals is not uniform, producing these population unities. In humans, culture is

another factor conditioning this organisation of human beings in groups or populations.

Therefore, in human population genetics, a population is a group of people of both

sexes, of all ages, that share the same territory, interbreed, and share common rules of

social behaviour and therefore, present a common genetic patrimony.


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Human population genetics studies the genetic differences, specifically, allele

frequency distributions between human groups and the mechanisms and processes that

generate, reduce, and change them as the result of ancient and/or recent demographic

events as well as differences in selective pressures.

I.5.1.1 Evolutionary processes

Population genetic variation is modulated by some factors called evolutionary

forcesdriving the evolution of living organisms. The current genetic variation found in

humans is the result of four evolutionary forces: mutation, selection, genetic drift and

gene flow (or migration). These processes can introduce variation (mutation) while

others remove it (selection, genetic drift). The study of these forces is complex and

requires mathematical models (Powell, 2005).

Mutation

A mutation is a change in a DNA sequence. Mutations can be caused by

mutagenic factors (radiation, viruses, and chemicals) or errors during meiosis or DNA

replication. A somaticmutation appears in any cell of the body, except the germ cells

(sperm and egg). These mutations are important in medicine as they can cause diseases

(as for instance, about 95% of all cancers). On the other hand, a germinal mutation is

the one that appears in the gonads and will be passed to the descendents. Population

genetics focuses on germinal mutations.

The mutation process is the only one that generates new variation (de novo

variation) as new alleles (mutations) appear. It is a random process, independent of the

effects and consequences. These new variants will undergo the effect of the other

evolutionary forces.

Genetic drift

Genetic drift is the random process by which the frequency of genetic variants

(alleles) fluctuates from one generation to the next due to the fact that the number of

genomes that pass to the next generation is only a sample from the genomes of the

previous generation. The effects of chance are directly related to population size. The


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probability of losing alleles is higher in small-size populations, generating greater

fluctuations and the reduction of the genetic variability over time.

The genetic drift is particularly important in two particular cases: 1) when

catastrophes (natural catastrophes, epidemics, wars) cause a drastic reduction of the size

of a population, called bottleneck, and 2) when a new territory is colonized by a small

population, which does not include all the variation of the original population, called

founder effect.

Selection

Natural selection refers to the differential reproduction of certain genotypes in

successive generations. That is, more adapted individuals will present a higher capacity

of survival, and therefore, will reproduce more than those not so well adapted. The term

fitness refers to this capacity of reproduction, more precisely, to the number of offspring

that reach sexual maturity, which is based on survival and fertility. The selection can

only act on the phenotype, not on the genotype. Selective pressure can be positive or

negative, favouring or acting against a certain phenotype, respectively.

Different subcategories of selection are distinguished. Sexual selection occurs

when a phenotype is preferred by the opposite sex potential partners, implying higher

chances of producing offspring. Ecological selection is the natural selection without the

sexual selection.

The patterns of selection (the effect of selection on phenotypes) can be: i)

disruptive, when the extreme phenotypes are favoured against intermediate ones, ii)

stabilizing, favouring the intermediate characteristics, and iii) directional, favouring one

extreme phenotype.

Migration

The movement of individuals from one population to another is known as

migration or gene flow, although in this last case, migrants must contribute to the next

generation. Migration affects the whole genome, which is the inclusion of genes into a

population from one or more populations. Migration cannot change allelic frequencies

at a species level but can change allele frequencies of populations. In the human

species, migration is particularly important due to its complex demographic history.


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I.5.2 Genetic markers

Human genetic variation among individuals and/or populations is studied using

polymorphisms. A polymorphism refers to the presence of more than one variant in alocus in a population. However, since we tend to reserve the term polymorphism for

when the less frequent allele has a frequency 1%, we use the more general term

genetic marker. The minor allele frequency (MAF) in a given population is the

frequency at which the rarest allele is present.

I.5.2.1 Brief description of the principal markers

There are different kinds of genetic markers regarding the amount of DNAinvolved, from a single nucleotide (sequence level) to whole chromosome(s)

(cytogenetic level). The most common studied polymorphisms provided by the DNA

from sequence to cytogenetic level are:

Single Nucleotide Polymorphisms (SNPs) are polymorphisms due to a base

substitution or an insertion/deletion of a single base. They are also called point

mutations.

Small insertions/deletions (INDELS/DIPS). Despite the fact that small

INDELs (ranging from 1 to 10kb) are highly abundant in humans and cause a

great amount of variation in human genes, they have received far less attention

than SNPs and larger forms of structural variation (see review Mullaney et al.,

2010).

Different types of INDELS are:

o Variable Number of Tandem Repeats (VNTR). These are genetic markers

characterized by the repetition in tandem of 2-6bp (microsatellites) or 10-

60bp (minisatellites). The microsatellites, also called Short Tandem Repeats

(STRs), have been the most widely used.

o Mobile elements represent a large amount of small INDEL variation in

humans. Transposable elements (TEs) are pieces of DNA from 300bp to

10kb that are able to jump from one location to another in the

chromosome. TEs are very diverse and are classified into two main groups

according to the mode of transposition: a) class I: retrotransposons, encode a


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reverse transcriptase (RT) and are restricted to eukaryote genomes, and b)

class II, DNA transposons, encode a transposase (Tnp).

Approximately ~45% (Figure 12) of the human genome can currently be

recognized as being derived from TEs, the majority of which are non-long

terminal repeat (LTR) retrotransposons, such as LINE-1 (L1), Alu and SVA

elements (Cordaux and Batzer, 2009).

Figure 12. The TE content of the human genome (Cordaux and Batzer, 2009).

Structural Variation. The large-scale genomic variation (>10 kb) includes

insertions, deletions, duplications, inversions and rearrangements of DNA

fragments of about several kilobases (kb) to megabases (Mb) (1kb-3Mb:

submicroscopic, >3Mb: microscopic) that are found in general population and,

apparently, have no phenotypic consequences for the carrier, although many of

these variants have been associated with diseases. Some authors have suggested

that Structural Variants (SVs) might have more impact in the phenotypic

variation than SNPs (Korbel, 2007). The main category of SVs is known as

Copy Number Variants (CNVs). CNVs are DNA segments of 1kb and an

average size of 250kb, present at variable copy number in comparison with a

reference genome. CNVs represent >15% of the human euchromatic genome

and differences between any two genomes can reach up to 15Mb. CNVs are


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found in humans and other vertebrates. They can vary in gene dosage (Conrad et

al., 2010).

Moreover, it is important to mention that different genomic compartments

present different features, providing different, although complementary information.

Uniparental markers are maternally (mtDNA) and paternally (Y chromosome) inherited

and do not recombine. They are useful in detecting ancestry and tracing population

movements, but, since they are just one locus, they are subject to stochastic errors. On

the other hand, autosomal chromosomes provide multiple ancestry information and

provide a more complete picture. Table 3 summarizes their characteristics.

Table 3. Genomic compartments from Cavalli-Sforza and Feldman, (2003).Genomic compartmentFeature

Autosomes X chromosome NRY mtDNA

Location Nuclear Nuclear Nuclear Cytoplasmic

Inheritance Bi-parental Bi-parental Uni-parental Uni-parental

Ploidy Diploid Haploid-diploid Haploid Haploid

Relative Ne 4 3 1 1

Recombination rate Variable Variable Zero Zero

Mutation rate Low Low Low High

I.5.2.2 Markers used in this work

In the present work different genetic markers have been determined, including:

Aluinsertions, SNPs, STRs, and the uniparental systems, mtDNA and Y chromosome.

Alu insertions

Aluelements are the most abundant short interspersed nuclear elements (SINEs),

representing, with approximately 1.1 million of Alu copies, more than 10% of the

human genome (Carroll et al., 2001) (Figure 12). TheAluname of these elements is due

to the presence of a recognition site for the restriction enzyme AluI in some members

(Houck el al., 1979). Typically, an Aluinsertion is a 300bp-long sequence ancestrally

derived from the 7SL RNA gene inserted into the genome through an intermediate RNA

single strand generated by RNA polymerase III transcription (Figure 13) (Batzer and

Deininger, 2002) and distributed throughout the genome of primates. These elements


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appeared some 65MY ago, when primates expanded and diverged (Deininger and

Daniels, 1986).

Figure 13. Mechanism of creation of anAluinsertion (Batzer and Deininger, 2002).

There is a small group of Alu elements called Master predisposed to the

retroposition (Deininger et al., 1992). During the evolution of these Alu elements,

mutations have appeared and have permitted the classification of these insertions into

12 subfamilies that have appeared at different times during the evolution of primates

(Roy et al., 1999) and are classified into ancient (Jo and Jb), intermediate, and recent

groups (Y, Yc1, Yc2, Ya5, Ya5a2, Ya8, Yb8 et Yb9) (Batzer and Deininger, 1991;

Carroll et al., 2001; Roy-Engel et al., 2001). Some members of the youngest

subfamilies are not yet fixed in humans and consequently are polymorphic for the

presence or absence of the insertion (Roy et al., 1999), known as Polymorphic Alu

Insertions (PAIs). Among these families, Ya5/8 and Yb8 include a large number of

polymorphic insertions; their frequencies vary among populations.


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Aluinsertions present several advantages that make them very powerful tools as

genetic markers for studying human evolutionary history and conduct human

population genetic studies (Stoneking et al., 1997; Batzer and Deininger, 2002; Cordaux

et al., 2007). PAIs are biallelic (insertion-lack of insertion) and considered as neutral

markers. Moreover, two noteworthy features are: 1) the insertion is identical by descent,

that is, when individuals share the same state at a locus it is almost certain to have

inherited it from a common ancestor (it is practica

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